# Allelic variants of IRKI contribute to photosynthetic efficiency by regulating rubisco activase in Populus

## TL;DR

A gene called IRKI in poplar trees boosts photosynthesis by regulating a key enzyme, rubisco activase, and a specific genetic variant improves plant growth.

## Contribution

Identified a causative gene IRKI and an elite haplotype module that enhances photosynthesis in poplar through molecular interactions.

## Key findings

- PtoIRKI-overexpression plants showed increased photosynthetic rate, starch content, and leaf area.
- PtoIRKI interacts with Rca to enhance rubisco activation and photosynthetic efficiency.
- The PtoHB1-PtoIRKIhap2-PtoRca module was validated as a target for improving photosynthesis in woody plants.

## Abstract

Photosynthesis directly determines plant biomass accumulation by controlling carbon flow and energy input. Thus, increasing photosynthetic efficiency is a promising approach for boosting plant growth and yield. However, the genetic basis of photosynthesis in perennial woody plants remains largely unknown, and the causative alleles warrant comprehensive investigation. Here, we performed a genome-wide association study (GWAS) on photosynthetic traits in a natural population of Chinese white poplar (Populus tomentosa). We identified inflorescence and root apices receptor-like kinase-interacting protein (IRKI) as a causative gene of photosynthesis that is significantly associated with the activity of rubisco activase (Rca). The seventh leaves of PtoIRKI-overexpression (OE) plants exhibited a 27.77% increase in net photosynthetic rate (Pn), a 31.42% rise in starch content, and a 16.83% expansion in leaf area compared to wild-type plants, whereas ptoirki-knockdown (KD) plants displayed the opposite phenotypes. Further analyses indicated that PtoIRKI interacted with PtoRca to enhance Rca activity, leading to increases in the activation state of ribulose bisphosphate carboxylase oxygenase (rubisco) and photosynthetic efficiency. Importantly, we identified an elite haplotype, PtoIRKIhap2, which exhibited higher PtoIRKI expression and Pn than PtoIRKIhap1. Finally, we found that homeodomain-leucine zipper protein 1 (PtoHB1) specifically bound to the PtoIRKIhap2 promoter, thereby promoting PtoIRKI expression and photosynthetic efficiency, as validated by integrating machine learning models and molecular experiments. Our results shed light on the molecular mechanism through which PtoIRKI modulates photosynthetic efficiency. We also provide an excellent haplotype module, PtoHB1-PtoIRKIhap2-PtoRca, that can be used to improve the photosynthesis of woody plants via molecular breeding.

The discovery of a gene–haplotype module that enhances photosynthesis in poplar reveals molecular targets for improving biomass in perennial woody plants.